Chuck vs the CIA
by sharpasamarble
Summary: AU1x1: Dark piece about a troubled time down the road for our favorite characters.
1. Unfamiliar Territory

_Ed. Note: Looking for a fluff piece? You're in the wrong place._

_This story does not fit into any existing timeline by myself or any other author._

_Standard disclaimers about Chuck not in any way belonging to me apply._

Sarah stared at the mirror, wondering if she was doing the right thing.

It was no longer a question of honesty. She had been honest with herself. More importantly, she finally was able to be honest with Chuck. That wasn't the issue.

The issue was that, more and more, she found her decisions as an agent were compromised because of her feelings for Chuck. As they had grown closer, she found her telling him things that she really shouldn't – talking about classified missions from her past, things going on in the agency, even going so far as to warn him that the Intersect 3.0 was coming online in Virginia. She always found ways to justify to herself why she would go against her instincts for Chuck. The last she justified under the umbrella of keeping him safe: he had to be on the lookout in case the NSA decided to try to take him out again. She was most definitely compromised.

The CIA knew all this; she had eventually felt obligated to report it. But by that point, Chuck had single-handedly taught them more about subliminal information implantation than all of their other experiments combined. He was almost unique in his ability to retain the information shown to him in The White Room. On his last "load" about three weeks prior, he had registered an unbelievable 99 percent retention rate of the entire contents of the system. When Project Omaha began, nobody thought that was possible.

Project Omaha had been her first assignment. Half the agents were there because they were anticipated to be excellent field agents; Sarah fell into that group. The other half were there for another reason: their cognitive skills supposedly would allow them to retain an inordinate amount of information. Teams were formed using one member from each group.

Unfortunately, most recruits in the latter group were brought in with only the single criterion in mind. Despite going through an inordinately long training period, most proved to be disasters as field agents, especially since none seemed to retain enough information to make a difference. Most either died in the field, or washed out altogether. Sarah wasn't sure what happened to the ones who washed out, but she doubted they were living happy lives anywhere.

The project had always been highly experimental – and controversial. The detractors worried that the agents might not recall any information until it was too late, and there was always a lag while the subject processed the triggering information. That little detail had nearly gotten her killed, although she didn't know what caused her partner to freeze up at the time.

The silver lining had been getting partnered with Bryce. He was one of the other agents in her group; she had always thought him a terrific agent, if a little arrogant and definitely not trustworthy. Still, when the program disbanded, he had personally requested her as a partner, which she found flattering given his undeniable skill.

As the years rolled along, the two went on dozens of successful missions together, and the pair became closer and closer. Inevitably, the two shared an incredibly passionate night together after a completed mission in Buenos Aires, and he became her first lover in years as well as the first person to touch her heart.

The two had been together for four months when Bryce mysteriously disappeared one night. All he left was a simple note: "It's hard to say goodbye."

The phrase, like so many others, was code. It meant that there was something he had to do, but he would be back. Except this time, things became extraordinarily complicated.

But that was all in the past now. What had seemed like disaster at the time had reminded her that Bryce ultimately couldn't be trusted and, ironically, led her to Chuck, Bryce's one-time best friend.

Juxtaposing thoughts of Bryce and Chuck, she was suddenly reminded of why she was doing what she was doing. When she thought of Bryce, she thought of a series of missions first and a set of passionate nights second. When she thought of Chuck, she thought of a series of everyday moments first and a set of missions second. Make that third; a trio of passionate nights that far eclipsed any spent with Bryce certainly trumped the missions as well.

Sarah looked at the picture of Chuck on her iPhone, his smile staring back at her and warming her heart. In so many ways, he was like a twelve-year old that had never grown up: all innocence, playfulness and uncorrupted goodness. She was absolutely doing the right thing; she knew it in her heart.

She set down the phone. Staring at her reflection in the mirror, she slowly lifted up the crown of the veil and placed it on her head, admiring the effect in the mirror. She felt almost … normal. Her smile dominated her face. There was no reason for any doubts.


	2. When Doves Fly Free

Outside, Casey, wearing an usher's suit, casually patrolled the outdoor seating area. The seating area wasn't large: there were little more than one hundred white wooden chairs meticulously arranged in rows, split down the middle by a path laid with fine pebbles. He seriously doubted even those chairs would be filled, but the people who were there made up for it with their happy laughter and joy for the upcoming nuptials.

He hadn't seated anybody personally, but the suit gave him a reason to be wandering the crowd and not seem out-of-place. Truthfully, neither he nor Sarah expected anything to happen, but that only made him look harder. He was almost superstitious about times like this: the least likely times were the best for an attack.

Completing his circuit of the crowd, he looked beyond the chairs to the two tents with the wide blue-and-white vertical stripes; the left one contained Bartowski and a trusted CIA agent while the right contained Walker. He suddenly realized that soon he was technically going to have to refer both of them as "Bartowski". He smirked; he had to needle them about that later.

Ellie and Morgan waited at the back; from her expression, Ellie clearly didn't mind that Morgan would be walking her down the aisle today. Staring at her for a second, he realized that nothing was going to ruin this day for her. She loved Sarah like a sister, and she couldn't be happier for the couple. On the other hand, Morgan looked like he might be the one to break down crying; he had moaned for weeks about losing his life partner.

The past two years had radically changed Casey, although it was difficult to see to the casual eye. He still maintained his cold, gruff demeanor almost out of habit, and there was certainly no love lost between him and many of the people his cover persona encountered on a regular basis. However, he had to admit, hanging around Chuck had helped him find his way back to himself.

Years of being an NSA killing machine had worn on Casey. He had always thought himself above being impacted by his years and years of assassinations, but looking back, only sheer force of will had kept him from snapping. The mission to help guard Chuck, seemingly such an annoying one at the beginning, had helped a semblance of his humanity to come crawling back from its deep level of repression.

Casey had cultivated a forest of bonsai trees at the suggestion of an NSA therapist. The idea was that the trees would give his mind something to help calm him while providing a peaceful focus. However, the hobby had not done nearly as much good as seeing some of the good people his work had helped. That helped bring perspective, and with perspective came the peace he so desperately sought.

Yeah, Chuck had a way of growing on you, kind of like mold. But Casey found he didn't really mind the guy, even growing to trust him enough to speak about some of his internal struggles about past missions, not the least of which was the NSA order to put Chuck in the ground. Ultimately, Casey had been unable to pull the trigger, and had instead helped Chuck destroy the Intersect 2.0, after Chuck had loaded the data into his mind. That kept Chuck essential, and ultimately the government chose not to hold a grudge. After all, they had tried to off the guy, so it would have been a little hypocritical. As long as Chuck was willing to help them learn and understand more about how his flashes work, he was an invaluable national resource. He was the key.

Casey checked his watch, and frowned. It was only a few minutes to the ceremony, and still no sign of Chuck. Guy was probably having a bout of indigestion or something. He instinctively reached for an earpiece that wasn't there; at Chuck's request, spy equipment had been strictly prohibited at the wedding. He wanted at least one day in his life to be as normal as possible. Still, Casey mused that he wouldn't be surprised to find Sarah had a sheath of knives strapped high on the thigh that didn't contain the garter. She was going to protect Chuck, no matter what.

No equipment meant no radio, so Casey would have to walk to Chuck's tent to find out what was delaying the groom. Scowling a bit, he started walking back up the center aisle, listening to the sounds of the crowd. Morgan and Lester were sizing up the crowd, but there were painfully few potential targets for their painfully inept advances; that was probably best for all concerned. Anna was making outrageously flirtatious faces at Morgan; apparently their on-again, off-again relationship was back on, at least for this week. Even Big Mike was there, looking dapper in a rented tux and a very attractive blond woman hanging on his arm.

Suddenly, a somewhat dismayed shout filled the air. A man stood up to his left, seemingly fixated on what was happening behind the flower-crusted arbor and the waiting efficient. Casey turned back around.

Somehow the cage holding the doves had come open early, and everyone was pointing at the birds were fluttering around the trees in the park-like area beyond the arbor. Casey gave an uneasy chuckle; that wasn't a good omen for a couple getting married. Still, he didn't really believe in omens. After watching the birds for a moment, he turned back to continue towards Chuck's tent.

A cell phone started ringing towards the back of the patrons. Up front, Devon stood up. "C'mon, guys; cell phones off. Interrupting the ceremony for a call would most definitely NOT be awesome."

Casey stopped and frowned as the phone rang a third time. He recognized that ring from somewhere. Then he placed it. "Chuck?!" he called out warningly.

Chuck's tent exploded as the NSA incinerator activated.

"CHUCK!!" he cried, his voice barely audible over the sudden screams in the crowd around him.

In the opposite tent, Sarah's face suddenly turned white to match her dress as she stood up. Casey's shout, the explosion, and the shocked silence of the crowd after the initial screams could only mean one thing. She wouldn't be getting married that day.

With unseeing eyes, she removed the veil from her head, her numb fingers letting the cloudy white fabric drift to the ground.


	3. A Needed Replacement

A young man sat in a chair in the center of The White Room, his vital signs displayed on a series of equipment via the contacts placed on key points of his body. His heart rate was up around 120.

He looked nervously up at Professor Fleming. "So, this won't hurt at all, right?"

The professor looked at him reassuringly. "Nope. It will put you in a kind of trance, and your mind will try to absorb all the information. Just relax and let it happen."

The subject, one of the professor's students from Stanford, still didn't look comfortable. He swallowed hard, and then nodded.

Fleming put on a pair of dark sunglasses, the same exact pair that Bryce Larkin once wore when he downloaded the secrets from the original Intersect. He tried not to get caught up in wondering for the umpteenth time how Bryce had come to possess the glasses that prevented the information from being absorbed; the glasses were a remarkable blend of materials that somehow disrupted the trance created by the series of encrypted images. Whoever created the glasses was some kind of genius.

He leaned down and pressed a button on the computer terminal. As the flow of images started, the Stanford student stiffened for the briefest of moments before slipping into a state of relaxation.

The professor smiled. That was exactly what was supposed to happen.

After making a quick check of the monitors, the professor studied the young man. This was the first subject who had come anywhere close to Chuck Bartowski's ability to retain information. Chuck had scored an unbelievably 98 percent on the subliminal image test in his class; this student had scored an 82 percent. No other student had ever cracked 60.

Still, the agency felt it was important to press forward on some of the ideas on image retention that Chuck had shared with them, so Fleming had recruited the student under the guise of a research project. The student spent the better part of three months working through mental exercises that Bartowski suggested would improve the retention capabilities. If he was able to retain at least 75 percent of the information in the Intersect, he would supposedly earn an entire semester's tuition.

The reality was, if he passed that test, he would likely be forcibly recruited. Director Graham and General Beckman were very nervous about the possibility of only having one human version of the Intersect; that made Chuck far too valuable. Chuck already seemed to realize this, given one or two of his demands during one of his recent visits. Reluctantly, Beckman and Graham had acceded to his demand to let Sarah and him marry, and they were worried about future demands he might make while they had no leverage on their side. If there was one thing the two of them couldn't abide, it was being blackmailed.

Shaking himself from his musings, the professor checked the subject's vitals again. So far, so good. He picked up the portable device that displayed the key vitals; absorption was likely to take hours, so he would check on the subject again later. He walked across the bright room, trying not to stare at the visual cacophony of images as he left the room.

A couple of hours later, he came back into the room. The patient's vitals still were good, but he didn't think it would hurt to check on the patient.

Walking back across the room, he heard a faint mumbling sound. That was unusual; Bartowski had always been completely quiet during the loading process.

The student was leaning to one side, staring at the images on the wall, his lips constantly moving. As Professor Fleming got closer, he could begin to make out some of the words, his sentences interrupting as the images changed.

"Orange Water was a covert operation to remove the head of a paramilitary rebel group in the Congo…"

"Iron Kettle is the code name for a double agent in the nation of Kazakhstan…"

"Nine different Chinese-American couples were sent to various regions in China to provide…"

The student's heart rate crept up a notch. He started leaning forward and backward in the chair. The tone of the young man's voice became more urgent.

The professor frowned; something was definitely wrong. He went over to shut off the images, but not before a couple more flashed on the walls.

"The South African diplomat to Switzerland is known to…"

"Velvet Curtain was a key part of the American …"

The professor shut off the images.

"Velvet Curtain."

"Velvet Curtain."

"Velvet Curtain."

The student continued to stare catatonically into space, rocking back and forth, arms wrapped around his sides. His heart rate increased again.

"Velvet Curtain."

"Velvet Curtain."

"Velvet Curtain."

Waving a hand in front of the student's face did nothing to bring him out of his trance. Something was very, very wrong.

The professor's last thought, just before the explosion ripped through the building, was to wonder whether Bartowski's theories had been incorrect.


	4. Reconciling Old Accounts

A young boy, just about to enter his teenage years, lay awake in his bed. It was almost midnight, but he was still up, reading a comic book under the tented blanket with the aid of a flashlight. His appetite for reading was voracious; he would often go through a book a day. Mostly he loved adventure stories, his favorites being tales of superheroes and spies.

An incriminating floorboard creaked ever-so-softly just outside his door in the hallway. He quickly shut off the flashlight and hid it under the covers with his comic. As the doorknob turned, he quickly lay down, assuming a normal sleeping posture for him. His parents, especially his mother, had caught him reading plenty of times because he was lying in an unusual position when they came to check on him. It had become something of a game to outwit them. He tried not to smile.

The door to his room slowly opened, a dim light from the hall casting a large rectangle on the wall opposite the bed. Through the ambient light, a slim female figure crept into the room, moving nearly silently across the floor of the hold house. The boy marveled at how adept his mother was at dodging the creaky parts of the floor; she was like a cat at times.

His mother gently sat down on the edge of the bed, carefully running her fingers through the boy's unruly hair. He thought he caught the sound of a faint sigh, but didn't dare open his eyes.

After a long moment, she said, "It's hard to say goodbye." She leaned down and gently pressed her lips to his forehead. Her departure disturbed neither the bed nor the suddenly ominous silence in the room.

When the door was shut once again, the boy leaned up on his elbows, puzzled at the words. What could she have meant by that?

He crept to the door, dodging the creaky floorboards just as his mother had and slowly slipped into the hall. A light from downstairs suggested somebody was awake; he carefully made his way to the top of the stairs and peeked through an opening in the banister. All he could see were the backlit silhouettes of his parents as they stood in front of the kitchen door.

His father's voice echoed up the stairwell. "You know you don't have to do this."

"And you know that's not true. They need me. You know I have no choice," his mother responded.

"What am I supposed to tell the kids?"

"You won't need to tell them anything."

"I think they'll notice if their mother just up and vanishes," he said wryly.

"Somebody will be here in a couple of hours. They'll inject me with something that will render me completely unconscious. Then they'll arrange the rest of the details."

A long silence followed. When his father spoke again, he sounded like his heart was breaking. "Please don't do this. I can't make it without you."

She put a comforting hand to his cheek. "Yes, you can. You have the strength."

Again, there was an uncomfortable silence. "Not without you, I don't," he said in a halting whisper, unable to look at her any more. He pulled the hand away and walked back across the room, collapsing into a chair.

Tears burned in the boy's eyes. He didn't know what was going on, but he could feel his family being torn apart. He crept back to his room as quietly as he could and climbed into bed. He cried for a long time, but sleep never really came.

Before the sun came up the next morning, he suddenly heard his sister bawling. It was a horrible, horrible sound. He leapt from his bed and ran downstairs, where a man wearing an ambulance driver's outfit was zipping up a bag on a gurney. His father was holding his sister close, but the act seemed to comfort neither of them. Tears streamed from his sister's eyes, while his father had a haunted look that suggested nothing would ever be right again.

Anger burned inside the young man as he stared at his mother being wheeled out the door in her artificially induced coma. As he helplessly watched his inconsolable father try to comfort his sobbing sister, he vowed to find the people responsible for this and to avenge the death of his family. All he could hear was the sound of his sister crying…

"Chuck?"

The voice brought him out of his memories. He reoriented himself; he was riding in the front seat of a red Corvette convertible, the breeze blowing through his hair on a beautifully sunny California costal highway. The sound of the engine, the spinning wheels, and the wind blowing across his ears created a pleasant white noise in his ears.

He looked down at the groundskeeper's suit he had slipped into in the tent. After injecting the CIA guard with a sedative, he activated the door to the dove cage. It had been a simple matter to slip out the back of the tent while everyone's attention was diverted. He had covered the twenty feet to the main building without anyone noticing before activating the NSA incinerator.

Chuck Bartowski was now dead.

He looked across at Bryce, noting the grin on his face. Bryce said, "I'm happy to report that the Intersect 3.0, along with their top scientist and likely all of your research, is no more."

Chuck allowed himself a wry grin. "That's OK; their research had a couple of problems that likely would have given them fits anyway."

While reporting his notions on image retention, Chuck had failed to mention a few things. Most notably, he had failed to mention that he had undertaken a series of mental exercises for the full five years while he was out of Stanford, not the three months he had suggested. That, along with a couple of other false leads, were likely to lead to fairly disastrous results for anyone attempting to load information into their minds.

Bryce had managed to obtain and share the CIA's original notes on the subject, but Chuck made a great deal of headway on his own. Actually, he was probably the world's foremost expert on the subject, especially now that Professor Fleming was dead.

When Bryce had been recruited to the CIA, he had quickly found out what they were recruiting him for. Bryce had a way of getting people to tell them more than they really should, and he quickly knew all there was to know about Project Omaha.

Bryce had no axe to grind with the CIA, but when Chuck suggested that they could be ridiculously wealthy inside of ten years, Bryce was quickly on board. Bryce wasn't long on scruples, and he always had an adventurous spirit.

After Professor Fleming's call to Chuck, the pair was tempted to allow Chuck to be recruited to Project Omaha. However, Chuck correctly suspected that the government scientists did not realize the full potential of the project, so they engineered the blow-up for two reasons: it gave Chuck time to research how to best prepare his mind to store the information, and to allay any suspicions because of their friendship when Bryce sent the Intersect to Chuck.

Chuck's mind was now full of 99 percent of the US government's classified database of secrets, including a set of intersecting data points that was no longer available to anyone but Chuck. At least, not until the Intersect 4.0 was built.

Soon Bryce would have his money. The pair had prepared aliases and a quiet little hideaway from which they planned to blackmail the American government for a ridiculous amount of money, just to keep the secrets hidden. If all worked out well, they would likely be looking at a nine-figure payout for staying hidden. And if the American government refused to budge, Bryce had enough contacts to help them make money in other ways.

Chuck had his revenge against the CIA. Not only was the Intersect destroyed, but he had severely compromised two of the government's best agents in the process. His carefully crafted persona was specifically designed to get Sarah and Casey to trust him, and even to help him to accomplish his goal. Their careers would likely be finished once the blackmail came to light.

He smirked at the irony. Sarah had asked him to trust her the night of their first "date", and consistently demanded his trust thereafter. She had been worried about the wrong thing: he completely trusted her from the start, especially because Bryce had fed him so much information about her. The problem was that she couldn't trust him.

They pulled off the highway and headed down to an inlet with a small harbor. They hopped out of the car and made their way across their dock, quickly preparing to cast off. Bryce stared a bit longingly at the car and the mainland, knowing he would likely never see either again. "I am going to miss a few things."

Chuck thought of Ellie and Morgan as he coiled up a rope and tossed it onto the deck. He had long prepared himself for this moment; he suspected both would understand if they knew the whole story. "Well, you know what they say."

Bryce grinned. "It's hard to say goodbye."

He reached out a hand and helped pull Chuck onto the deck, clasping Chuck on the shoulder. He quickly made his way to the captain's chair and, after a couple of quick checks, threw the throttle forward.

Chuck let out a whoop and raised his hands over his head in victory as the boat took off for the open sea.


End file.
